List of Ho-Oh Counters

All usable movesets are listed. The movesets are ranked from best to worst (out of the usable movesets), left to right.

Non-Solar Beam:
1: Golem (RT/SE, RT/RB, RT/AP*)
2: Omastar (any moveset without Mud Shot, rock ones are better than water)
3: Raikou (TS/WC, TS/Tb)
4: Zapdos (CB/Tb, CB/ZC)
5: Tyranitar (B/SE)
6: Vaporeon (WG/HP, WG/AT) Tank
7: Dragonite (any moveset without Steel Wing)
8: Gyarados (DT/HP, B/HP, DB/HP*)
9: Lugia (ES/HP, DT/HP) Mega-tank

Solar Beam:
1: Zapdos (CB/Tb, CB/ZC)
2: Raikou (TS/WC, TS/Tb)
3: Dragonite (any moveset without Steel Wing)
4: Gyarados (DT/HP, B/HP, DB/HP*)
5: Golem (RT/RB, RT/AP*, RT/SE)
6: Lugia (ES/HP, DT/HP) Mega-tank
7: Vaporeon (WG/AT, WG/HP)

* Legacy moves

The reason why the optimal movesets for Golem and Vaporeon are different for Solar Beam is because they are weak to Solar Beam. So if they use single bar charge moves, they might not get their charge move off.

Edit: Missed out Dnite and Ttar, added them in